June 2011 Commit Log

Number of Commits:
38
Number of Active Developers:
1
westram 2011-06-29 15:57 Rev.: 7674


* nameserver
- fixed a bug introduced with [7304]
* second part of fullname was always truncated
- bug above revealed another OLD bug
* if the used part of the fullname was shorter than 3 chars, the generated shortname was not stored
- so it was used again for the next similar fullname, resulting in duplicate names

3 lines of code changed in 1 file:

westram 2011-06-28 11:05 Rev.: 7673

do not fail if directory-to-delete is already missing

1 lines of code changed in 1 file:

westram 2011-06-16 22:23 Rev.: 7669


* merge from dev [7638] [7639] [7646] [7645] [7647] [7648] [7649] [7650] [7651] [7652]
- compatibility with cppcheck 1.49 (assert + ASSERT_RESULT)
- fixed (AWT and WINDOW)
* missing const attributes
* uninitialized/unused/wrong-scoped/useless variables
* alloc/free/delete mismatches
* use assertions instead of null-pointer-assignments
- removed
* AW_device_Xm fast/slow/fastflag
- new class AW_scalar
* can hold any AW_awar-value
- uses int32_t (AW_awar is based on GB_INT which is 32 bit)
* knows its type
* use in
- AW_option_struct / AW_toggle_struct (both classes were identical -> replaced them by new class AW_widget_value_pair)
- in AW_variable_update_struct (now !VarUpdateInfo)
- in AW_select_table_struct (now AW_selection_list_entry)

598 lines of code changed in 42 files:

westram 2011-06-16 22:12 Rev.: 7668


* merge from dev [7578] [7579] [7580] [7581] [7582] [7585] [7587] [7588] [7589] [7592] [7593] [7594] [7595] [7596] [7597] [7598] [7599] [7601] [7602] [7603] [7604] [7605] [7606] [7607] [7608] [7609] [7610] [7611] [7613] [7615] [7616] [7618]
- ARB canvas printing
* generate xfigs with 1200 dpi (was 80)
* DRYed canvas_to_xfig vs canvas_to_printer
* tracked down a bug in fig2dev causing wrong prints (added a workaround plus toggle to disable it)
* paint invisible to printer (as white dots)
- print two invisible dots which enclose the area calculated by size-device (-> fig2dev centers correctly)
* fixed magnification
- replaced hardcoded border with a relative border around the overall figure and a relative non-printable page-border
- use these borders for xfig-export and printing (previously only used in xfig-export)
- rewrote overlap calculation
* dialog
- missing macro-id for 'Fit on'
- provide paper sizes and pass them to fig2dev
- display resulting output-size of figure in print dialog
- added quick-fit buttons several page count
- added 'lock to pages'
- refactorings
* AWT_canvas
* AWT_graphic
* AWT_graphic_exports
* AWT_nonDB_graphic
* AW_device_size
- canvas draw function
* line styles (AW_DOTTED, AW_DASHED)
* changed line_width to short (assert line_width is > 0)
* fix missing final pixel on lines/boxes
* fix width/height of XFillRectangle
* changed cap_style + join_style
* changed code drawing boxes with fixed pixel width (due to correct lines/boxes)
- added AW_device::rtransform_pixelsize().
- rewrote IRS display
* uses double instead of int
* scroll closed groups inside top-folding-area until they are completely scrolled out of main-area
* draw one thick line for folding-separator
- do only draw on print device, if printing screen-only
* group frame/box
- draw dotted frame on unfolded groups
- frame/box size represents depth and size of subtree (as in dendrogram)
* condensed display
* draw text on size device
- enhanced AW_device_size
* tracks size info separately for scalable and unscalable gfx-elements
* reset() sets clipping to a BIG area on size device to avoid clipping (size should NEVER EVER be clipped)
* AW_device
- recalc_size() uses unscalable overlap caused by text at borders of graphic to dynamically set some extra padding
- replaced ALL default paddings by constant value (10 pixel)
- when a zoom-reset is done now, ARB correctly fits the graphic AND the text into the viewport
- unit tests (tree display)
* use monospaced font (makes faked font-limits more accurate)
* changed zoom/area calculation
* draw 2 boxes (one around gfx-text, another around gfx+text)

12482 lines of code changed in 47 files:

westram 2011-06-16 20:38 Rev.: 7667


* merge from dev [7576] [7577] [7584] [7586] [7617]
- fix 'unused param' and 'unused variable' caused by NDEBUG (only used in assertions)
- hide functions testing assertion failures when no assertions are used
- disabled dumping macro execution
- GBS_strstruct
* alternative ctor specifying initial buffersize
* equivalent nprintf() for GBS_strnprintf on class level
* rename (vprintf -> vnprintf)
- PT_SERVER: when some species were missing data in default-alignment, progress failed

69 lines of code changed in 15 files:

westram 2011-06-16 19:16 Rev.: 7666


* merge from dev [7539] [7541] [7543] [7544] [7548] [7549] [7550] [7552] [7553] [7554] [7555] [7556] [7557] [7558] [7559] [7561] [7562] [7563] [7564] [7565] [7566] [7567] [7568] [7569] [7570] [7571] [7572] [7574] [7575]
- behavioral changes
* when jumping to gene the text will also move into viewport
* this slightly changed the zoom used in IRS tree
* dont try to draw clipped bracket
* arcs were not drawn if NW-quadrant was not fully visible
* fixed '~'-bond (SECEDIT): use constants; fixed a small gap sometimes visible; reduced OUTSIDE overhang of arcs by 15 degrees
* reset disp_device after show()
- use new type AW_rgb for colors
- removed old-style enum typedefs
- refactored
* AW_GC
* DRYed AWT_graphic_tree::show() vs fake_AWT_graphic_tree::test_show_tree()
* AW_clipable
* moved font_overlap values into AW_font_overlap
* AW_device
- removed transform/rtransform flavors using ints (replaced usages by Position/Rectangle transformations)
- added get_rtransformed_cliprect
- pass radius as Vector (circle/arc)
- fixed degrees chaos in arc params: arc_degrees now also is clockwise (like start_degrees) - both are clockwise cause ARBs y-coordinate grows downwards
- invisible_impl uses Position as param
- fixed return type of draw functions
- fixed a bug in pop_clip_scale
* push+pop did not restore scale and offset properly (only if zoom was not 1.0)
* reset AW_zoomable before restoring and restore offset before scale
- AW_device_Xm
* refactored arc_impl
- AW_device_print
* refactored circle_impl
- added assertion against drawing zero-sized circles
- test for positive radius before drawing bootstrap circles (e.g. if branchlength is zero)
- "fix" clipping of circles on AW_device_print (only affects printing when "screen only" is selected)
* if more than half of circle gets clipped -> skip circle
* otherwise force circle into clipped bounding rectangle (i.e. print a smaller circle, that fits on the screen)
* basic implementation of AW_device_print::arc_impl
- arcs based on circles are drawn using xfigs ARC command
- arcs based on ellipses are interpolated using splines
- clipping does some as with circles (clip bounding-box and draw arc inside; if less than half of arc is inside clipping area, skip arc completely)
* separated fprintf into single lines for better documentation of single xfig parameters
* AW_area_management (made member variables private + split up with useless friends)

9010 lines of code changed in 46 files:

westram 2011-06-16 18:30 Rev.: 7665


* merge from dev [7546] [7547] [7583] [7600]
- AW
* added Vector / !LineVector :: is_horizontal / is_vertical
* made Angle(double) explicit
- added double versions of set_rel_angle and set_abs_angle to SEC_oriented
- SEC_segment::paint might be faster since it now uses faster Angle addition
* before it recalculated sin/cos of step-angle inside loop
* dump functions for Position, Vector, !LineVector, Rectangle

47 lines of code changed in 4 files:

westram 2011-06-16 16:16 Rev.: 7664


* merge from dev [7509] [7510] [7511] [7514] [7517] [7520] [7524] [7527]
- updated demo.arb (for treedisplay unit-tests)
* updated POS_VAR_BY_PARSIMONY
* calculated upper bootstrap limits
* show bootstrap circles
* select a species which is member of the default tree
- added unit-tests for tree display
- fixed source-list

306 lines of code changed in 8 files:

westram 2011-06-16 15:58 Rev.: 7663


* merge from dev [7516] (cleanup 'export to xfig': help/buttons/menu entries)
- part already merged with [7661]

34 lines of code changed in 2 files:

westram 2011-06-16 15:48 Rev.: 7662


* merge from dev [7518] [7519] [7521] [7523] [7525] [7526] [7528]
- flip a few line coordinates (only changes line orientation)
- AWT_graphic_tree
* refactored show_dendrogram()
* x_cursor / y_cursor -> Position cursor (-> private)
* eliminated class-member y_pos (temporary used for calculation). Functionality moved into parameter 'pen' of show_dendrogram
* renamed some memfuns
* IRS
- explicitely set grey_level before drawing boxes
- dont pass device to show_irs_tree (use AWT_graphic_tree::disp_device)
- removed irs_gl.device (duplicate of AWT_graphic_tree::disp_device)
- renamed irs_gl->IRS
* added set_line_attributes_for
* do not pass down linewidth in show_radial_tree
* removed dead code
- AP_tree
* added set/get_linewidth
* removed inline functions with same functionality
* rename reset_line_width -> reset_child_linewidths

359 lines of code changed in 7 files:

westram 2011-06-16 15:10 Rev.: 7661


* merge from dev [7512] [7520] [7522] [7529] [7530] [7531] [7532] [7535] [7536] [7537] [7538]
- replaced several '-1' by AW_NO_COLOR
- don't save undefined colors into xfig
- AW_GC
* color (short->unsigned long)
* added reset
* inlined and renamed some functions
* added possibility to freeze the defaults for a gc
- AW_stylable
* added reset_style()
* rename set_fill -> set_grey_level
- extracted AW_GC_set out of AW_common
- rename AW_rectangle -> AW_screen_area to indicate its using screen coordinates (int)
- removed various flavors of AW_device::get_area_size()
- attempt to fix strange !LineVector(AW_screen_area)-ctor (which decrements size by 1)
- added bounding_box() inlines for all combinations of Rectangle / !LineVector / Position
- moved AW_INT()

328 lines of code changed in 31 files:

westram 2011-06-16 13:23 Rev.: 7660


* merge from dev [7513] [7515]
- AW_device_print
* use AW_INT()
* changed line cap-style (0->1) => smoother display at "connections" of single lines

12 lines of code changed in 1 file:

westram 2011-06-16 13:03 Rev.: 7659


* merge from dev [7494] [7495] [7496] [7497] [7498] [7499] [7500] [7501] [7502] [7503]
- separated X and ARB a bit
* added base classes
- AW_GC (from AW_GC_Xm)
- AW_common_Xm (from AW_common)
* the class names are misleading, since they are X- not Motif-dependent
- refactored
* AW_device
* AW_clip (now AW_clipable)
* AW_matrix (now AW_zoomable)
* AW_gc (now AW_stylable)
- bugfixes
* set_lineattributes() did not set given line style at all. It has been impossible to paint dotted lines
* leak in AW_common-dtor
- changes
* AW_font_limits (tracks min char width)
* AW (!LineVector/Rectangle) ctors

670 lines of code changed in 22 files:

westram 2011-06-16 11:39 Rev.: 7655


* merge from dev [7485] [7493]
- eliminated AW_font_information (using AW_font_limits)

123 lines of code changed in 13 files:

westram 2011-06-16 09:01 Rev.: 7653


* forgot to delete old iupac module in [6830]
* replace null-pointer-assignments by assertions

20 lines of code changed in 6 files:

westram 2011-06-15 12:27 Rev.: 7644


- note about default config.makefile
- fix redirection

2 lines of code changed in 1 file:

westram 2011-06-15 12:16 Rev.: 7643


- make executable

1 lines of code changed in 1 file:

westram 2011-06-15 12:14 Rev.: 7642


- script to compile ARB (name fix)

6 lines of code changed in 1 file:

westram 2011-06-15 11:51 Rev.: 7641


- script to compile ARB

144 lines of code changed in 1 file:

westram 2011-06-15 06:50 Rev.: 7640


- progress was missing title when called from ali-admin

1 lines of code changed in 1 file:

westram 2011-06-13 22:53 Rev.: 7637


* Mark by reference
- default to error, if field is not present (added toggle)
- postprocess references field content through ACI
* added example postprocessing for selected (hack, works for species only)

211 lines of code changed in 4 files:

westram 2011-06-13 18:23 Rev.: 7636


* added basic reference entries handler
- goal: perform action on all items referenced by a field of some items
* added NTREE/Species/Mark by reference (basic functionality)
* moved !SpeciesSet to DBItemSet
* deleted dead module-fragment AWT_automata

392 lines of code changed in 13 files:

westram 2011-06-13 18:04 Rev.: 7635


- AWT_QUERY_RANGE has to be passed to ad_item_selector::get_first_item/get_next_item

149 lines of code changed in 7 files:

westram 2011-06-13 18:02 Rev.: 7634


- suppressing warnings suppressed errors instead

19 lines of code changed in 1 file:

westram 2011-06-12 10:54 Rev.: 7633


* added new target 'dep_graph'
- builds many gifs showing lib-dependencies
- resolve CROSS_LIB early
* needs_libs.pl
- able to resolve dep->lib
- define maxsize for output graph (17!'')
- allow multiple targets when building graph

153 lines of code changed in 3 files:

westram 2011-06-11 18:42 Rev.: 7632


* ARB_DIST
- use ints in DI_dmatrix
- matrix allows much denser display
* changed cell-dimensions for matrix display
- fixed calculation of dimension
* use correct gc for different cell types
* use MUCH smaller cell padding
- changed rulers for range display
* use 4 instead of 5 units
* every 2nd unit is half-sized
* rulers fit better into cell-space
* scroll callbacks
- DRYed
- allow text-overlap on clip-borders (old version worked around the broken scrollers with big padding)
* "real" identity cells (i.e. if species is identical) now show "---" instead of "0.0"
* examples
- [attachment:ticket:152:condensed_matrix.gif extremely condensed matrix] and
- [attachment:ticket:152:condensed_matrix_readable.gif readable condensed matrix]
- removed refresh on focus callback
- several matrix display options are configurable
* padding
* leading zero and no of digits
* name characters shown
- added menu 'Range' containing predefined ranges
* added two new ranges (species=2%, genus=5%)

333 lines of code changed in 4 files:

westram 2011-06-11 15:18 Rev.: 7631


- cosmetics

2 lines of code changed in 2 files:

westram 2011-06-11 13:19 Rev.: 7630


- fix 'make clean && make help' (thx to Elmar)

3 lines of code changed in 1 file:

westram 2011-06-11 12:19 Rev.: 7629


- ARB_DIST
* short explanation of 'compressed matrix'

11 lines of code changed in 1 file:

westram 2011-06-10 20:01 Rev.: 7628


* when error during save occurred, error message was destroyed before it was shown
* changed some save error messages

8 lines of code changed in 2 files:

westram 2011-06-10 15:11 Rev.: 7626


* merge from dev [7533] [7534] [7542] [7551]
- automatically create interdiff.patch after creating new patch

9 lines of code changed in 1 file:

westram 2011-06-10 15:06 Rev.: 7625


* merge from dev [7480] [7481] [7483]
- valgrinded SEQ_QUALITY
- fixed op= (SQ_GroupData_RNA and SQ_GroupData_PRO). Now returns *this
- fixed PersistantFlag::op=

52 lines of code changed in 9 files:

westram 2011-06-10 15:01 Rev.: 7624


* merge from dev [7473] [7474] [7475] [7476] [7477] [7478] [7479]
- NTREE
* rewrote main (CLI parsing, handling different ways to startup)
* some refactorings
* show com-error-reason on startyp ("THIS PROGRAM HAS PROBLEMS TO OPEN INTERCLIENT COMMUNICATION...")
* activated arb functions attributes
* added awt_execute_macro (execute a macro by name)
* added new CLI switch --execute (runs a macro after startup)
* DRYed load_and_startup_main_window vs start_main_window_after_import
- ARBDB
* gb_local_data keeps track of opened/closed DBs
* added GB_shell4perl (automatically closes all open databases on exit; macros working again)
- removed dead code (macro related)

541 lines of code changed in 21 files:

westram 2011-06-10 14:50 Rev.: 7623


- merge from dev [7450] [7452] [7456] [7457] [7458] [7459] [7460] [7461] [7464] [7465] [7466] [7467] [7468] [7469] [7482]
* tweaked compiler options
- activated -Weffc++
* postfilter warnings where Scott Meyers' advices are too general.
- base classes should not always have virtual destructors, since that renders tiny classes useless and
- members should not always be initialized via initialization list, since that often violates the DRY principle
* fix gcc's inability to detect that Noncopyable implements a private copy-ctor and op=
* this slows down complete ARB recompilation by ~5%
- added -Wold-style-cast (inactive)
- removed -Wno-non-template-friend added in [7447]
* postcompile.pl
- added option --original to show unmodified compiler output
* declared op= for classes which had a copy-ctor
* moved op= macros to arbtools.h
* derived classes containing pointers from Noncopyable (use Noncopyable virtually) or
* made them copyable if needed (awt_mask_item, KnownDB, Code, AWT_registered_itemtype, GEN_gene, !PosGene, !PartialSequence, !PlugIn, Range, Convaln_exception)
* other related changes
- user mask destruction working now

1066 lines of code changed in 227 files:

westram 2011-06-10 14:24 Rev.: 7622


* merge from dev [7434] [7435] [7436] [7437] [7438] [7439] [7440] [7441] [7442] [7443] [7444]
- AW_device
* removed some derived-class-specific functions
* virtual functions
- removed default parameters, renamed them to XXX_impl, made them private and added missing variants to replace direct calls to renamed functions
* added AW_simple_device as base for AW_device_click and AW_device_size
* do not pass AW_CL/AW_CL for AW_device_click down through all paint functions, instead create instances of AW_click_cd
* devirtualized ready_to_draw + cursor
* added default for filter to all paint functions (removed default from calls)
* XXX_impl functions use Position, Rectangle, Vector etc. instead of AW_pos
- AW_common
* removed unneccessary members; made members private
* moved some code between AW_gc, AW_GC_Xm and AW_common
* global data (color tables) now referenced by references instead of pointers
* made independent member function x_alignment() global
* no longer install resize callback from ctor
- AW_clicked_line (renamed some members; removed distanceTo)
- fixed possible return of temporaries
- AW_root
* made independent member functions font_2_ascii() and font_2_xfig() global (AW_font_2_ascii AW_font_2_xfig)
- Tree display
* client data changed (bootstrap text and vertical lines starting at bifurcation belong to son now)

1278 lines of code changed in 47 files:

westram 2011-06-10 13:55 Rev.: 7621


* merge various small fixes from dev [7445] [7446] [7447] [7449] [7451] [7454] [7455] [7462] [7463] [7470] [7471] [7472]
- compile fixes
* AISC now depends on AISC_MKPTPS
* tweaked compiler options
- added -fno-common
* puts all global data symbols into data section (instead of common blocks)
* duplicated data-symbols now lead to link-errors
- added two C++-warnings
* run POST_COMPILE when compiling server/client libs
* do 'checks' from 'build'
- code fixes
* close 2 unclosed files
* dont misuse GB_export_errorf in user masks
* fixed assertion failure in GB_remove_callback (removed callback from inside callback)
- user masks were not properly unlinked from DB before DB got destroyed
* close DBs
- when opening import window after startup
- before quitting merge tool
* fixed assertion failure in NT_fix_dict_compress
- after fresh import there were no affacted keys and progress failed. Skipped whole repair section
* skip empty subcounter
* clear 'alignment not found' error

89 lines of code changed in 12 files:

westram 2011-06-10 13:20 Rev.: 7620


- merge from dev [7432] [7433]
* removed AW_ERROR_BUFFER, AW_ERROR, aw_error, aw_errorbuffer_message
* replaced by GBS_global_string / aw_message / GBK_terminate / assert / ...
* added AW_awar::assert_var_type()

157 lines of code changed in 18 files:

westram 2011-06-10 09:38 Rev.: 7619


- merge [7612] from dev

56 lines of code changed in 1 file:

May 2011 »

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